fork/cellxgene
1
0
Fork 0
mirror of https://github.com/chanzuckerberg/cellxgene.git synced 2026-10-09 05:58:11 +08:00
Code Issues Packages Projects Releases Wiki Activity

clean up type inferencing (#2332)

Browse Source 
* unit tests for 64 bit conversion

* clean up type handling

* type inference tests

* more type inference fixes

* use schema to determine user intent for data typing

* stop using deprecated API

* fbs type encoding test

* add missing test

* add more tests

* correctly infer X type for CXG adaptor

* lint

* fix typo

* ts migration

* cleanup from PR review

* lint

* PR review changes
This commit is contained in:
Bruce Martin
2021-07-28 15:10:12 -07:00
committed by GitHub
parent 1140676106
commit 32f60a1547
15 changed files with 730 additions and 346 deletions
Download Patch File Download Diff File Expand all files Collapse all files
backend/czi_hosted/data_anndata/anndata_adaptor.py
+13 -9
View File
@@ -66,11 +66,11 @@ class AnndataAdaptor(DataAdaptor):
@staticmethod
def _create_unique_column_name(df, col_name_prefix):
""" given the columns of a dataframe, and a name prefix, return a column name which
does not exist in the dataframe, AND which is prefixed by `prefix`
"""given the columns of a dataframe, and a name prefix, return a column name which
does not exist in the dataframe, AND which is prefixed by `prefix`
The approach is to append a numeric suffix, starting at zero and increasing by
one, until an unused name is found (eg, prefix_0, prefix_1, ...).
The approach is to append a numeric suffix, starting at zero and increasing by
one, until an unused name is found (eg, prefix_0, prefix_1, ...).
"""
suffix = 0
while f"{col_name_prefix}{suffix}" in df:
@@ -124,7 +124,11 @@ class AnndataAdaptor(DataAdaptor):
def _create_schema(self):
self.schema = {
"dataframe": {"nObs": self.cell_count, "nVar": self.gene_count, "type": str(self.data.X.dtype)},
"dataframe": {
"nObs": self.cell_count,
"nVar": self.gene_count,
**get_schema_type_hint_of_array(self.data.X),
},
"annotations": {
"obs": {"index": self.parameters.get("obs_names"), "columns": []},
"var": {"index": self.parameters.get("var_names"), "columns": []},
@@ -201,10 +205,10 @@ class AnndataAdaptor(DataAdaptor):
self.parameters.update({"diffexp_may_be_slow": True})
def _is_valid_layout(self, arr):
""" return True if this layout data is a valid array for front-end presentation:
* ndarray, dtype float/int/uint
* with shape (n_obs, >= 2)
* with all values finite or NaN (no +Inf or -Inf)
"""return True if this layout data is a valid array for front-end presentation:
* ndarray, dtype float/int/uint
* with shape (n_obs, >= 2)
* with all values finite or NaN (no +Inf or -Inf)
"""
is_valid = type(arr) == np.ndarray and arr.dtype.kind in "fiu"
is_valid = is_valid and arr.shape[0] == self.data.n_obs and arr.shape[1] >= 2